I am running MOTHUR with already submitted metagenomic sequences in SRA. In that case I am not getting any "MOCK" community sequences (as given in SOP). Should I run without "MOCK" sequences?
The mock community is a nice control to have, basically you sequence a community with a known distribution of species and make sure that at the end of the process you get the desired results. Most of the experiments I know of don't use mock communities and just rely on the pipeline to work well so to answer your question, you can run mothur without a mock community.